Metabolomics Software Tools. Xiuxia Du, Paul Benton, Stephen Barnes
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1 Metabolomics Software Tools Xiuxia Du, Paul Benton, Stephen Barnes
2 Outline 2 Introduction Software Tools for LC-MS metabolomics Software Tools for GC-MS metabolomics Software Tools for Statistical Analysis
3 Introduction LC-MS data analysis workflow GC-MS data analysis workflow data preprocessing feature extraction statistical analysis deconvolution statistical analysis compound identification compound identification pathway analysis pathway analysis 3
4 Software Tools for LC-MS Commercial MassHunter Agilent MetQuest Thermo Scientific MetWorks Thermo Scientific Multiple Mass Defect Filter Thermo Scientific Progenesis QI Waters XCMS plus Sciex and more 4
5 Software Tools for LC-MS Free Insilicos Viewer ProteoWizard SeeMS: interactive viewer for mass spec data files (Windows only) MSConvert: convert between various file formats MZmine 2: LC-MS data processing MetaboSearch: perform mass-based metabolite search simultaneously against four major metabolite databases MetaboAnalyst: a web server for metabolomics data analysis and more 5
6 Data format Proprietary data formats: need vendor library functions to access Open data formats: free library functions to access netcdf mzdata mzxml mzml Company File extension Agilent.D Sciex Theomo Waters.WIFF.RAW.RAW 6
7 InsilicosViewer 7
8 Insilicos Viewer Raw data viewer total ion chromatogram MS and MS/MS 8
9 ProteoWizard 9
10 ProteoWizard: SeeMS A data viewer Can read these open data formats mzml mzxml 10
11 ProteoWizard: SeeMS Raw data viewer total ion chromatogram spectrum list of scans 11
12 ProteoWizard: MSConvert Data format converter 12
13 ProteoWizard: MSConvert Supported data formats Read: open formats, vendor formats Write: open formats Filters and transformation mslevel Peak picking Zero samples ETD filter Threshold peak filter Charge state predictor Activation Subset 13
14 MZmine 2 14
15 MZmine 2 LC-MS metabolomics data processing, analysis, and visualization Supported open data formats NetCDF mzdata mzml mzxml 15
16 Raw data import list of scans in raw files MS scans in blue MS/MS scans in red # sequential retention time MS level type of spectrum p = profile c = centroid t = thresholded polarity of ionization + = positive - = negative? = unknown 16
17 Raw data visualization brings up Right click on the file name 17
18 Raw data visualization double click TIC total ion chromatogram brings up spectrum 18
19 Raw data visualization 2D view 19
20 Raw data visualization rotate to find the best perspective 3D view 20
21 Data pocessing Workflow Raw data import (optional) Raw data methods / Filtering Peak detection Isotopic peak grouping (optional) Identification of fragments, adducts, and peak complexes (optional) Normalization of retention time Alignment (optional) Gap filling (optional) Normalization of peak heights / areas (optional) Identification using database search, formula prediction, etc. Data analysis and export 21
22 Peak detection Mass detection Centroid Exact mass Local maxima Recursive threshold Wavelet transform Chromatogram building Peak deconvolution 22
23 Peak detection Peak detection procedure 23
24 Mass detection Mass detection options click here to bring up the parameter window 24
25 Mass detection Set mass detection parameter 25
26 Mass detection Set mass detection parameter 26
27 Chromatogram building Chromatogram builder 27
28 Chromatogram building Chromatogram builder set parameters 28
29 Chromatogram building After chromatograms are built peak list # ID m/z retention time 29
30 Chromatogram building To display extracted ion chromatograms brings up Right click on the file name 30
31 Chromatogram building Show chromatogram information 31
32 Chromatogram building Show chromatogram information a particular extracted ion chromatogram (EIC) 32
33 Peak deconvolution 33
34 Peak deconvolution Algorithms 34
35 Peak deconvolution Set parameters click here to bring up the parameter window 35
36 Peak deconvolution deconvolution finished 36
37 Peak deconvolution Results 37
38 Alignment Retention time normalization 38
39 Alignment Retention time normalization: set parameters
40 Join aligner Alignment
41 Join aligner: set parameters Alignment
42 Get aligned peak list Alignment
43 Alignment Information on aligned peak list Green: present Red: absent
44 Peak identification Options 44
45 Peak identification By searching custom databases an example custom database 45
46 Peak identification By adduct search: set parameters 46
47 Adduct search results Peak identification 47
48 By online database search Peak identification 48
49 Peak identification Online database search results 49
50 Options and parameters Gap filling 50
51 Gap filling Results and visualization options 51
52 Set visualization parameters Gap filling 52
53 Gap filling Visualization 53
54 Data analysis Options 54
55 Data export Options 55
56 Data export Parameters 56
57 Data export csv format 57
58 MetaboSearch 58
59 MetaboSearch Input data format 59
60 MetaboSearch GUI 60
61 MetaboSearch Steps 61
62 Software tools for GC-MS Metabolomics 62
63 Software Tools for GC-MS Commercial ChromaTOF LECO MassHunter Agilent Free AMDIS: Automated Mass Spectral Deconvolution and Identification System NIST MS Search Tagfinder 63
64 AMDIS Raw data visualization 64
65 AMDIS Result visualization 65
66 NIST MS Search GUI 66
67 Software tools for Statistical Analysis 67
68 Stats and Machine Learning Commercial SIMCA Mass Profiler Professional (MPP) Agilent and more Free MetaboAnalyst R 68
69 MetaboAnalyst 69
70 Other software tools COMSPARI COMparison of SPectral And Retention Information MathDAMP Mathematica package for Differential Analysis of Metabolite Profiles MSFACTs and many more Metabolomics Spectral Formatting, Alignment and Conversion Tools 70
71 Thank You
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